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Detection of porcine species DNA on meat processed food samples (shredded meat) using Real-Time PCR Alfi Sophian; Sri Utaminingsih; Tirta Setya Bhakti; Dewi Rahmawati
Journal of Halal Product and Research (JHPR) Vol. 5 No. 1 (2022): Journal of Halal Product and Research (JHPR)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jhpr.vol.5-issue.1.32-37

DNA detection of porcine species in processed meat samples (shredded meat) was carried out as an effort to enrich the literature and reference alternative testing methods in the control of halal products circulating in Indonesia. The purpose of this study was to detect the DNA of porcine species in samples using real-time PCR. The research method used is a qualitative technique. This technique analyzes the CT value of the sample compared to the positive control by looking at the formation of the sigmoid curve if amplification occurs. The controls used consisted of negative control, positive control, other DNA control, and LOD control. The extraction technique used is the column centrifuge technique. The extraction results were then measured using a nano photometer to see the purity and concentration of the extracted DNA. Based on the research, it is known that the extraction results read on a nanophotometer at a wavelength of A260 / A280 show a concentration of 24,350 with a purity value of 21,164. For sample testing, the results of real-time PCR analysis showed the sample was detected at CT 39.77, positive control at CT 31.66, and LOD at 28.32. for negative control and specificity using other DNA was not detected. The conclusion of this research is that the sample used can be detected by the presence of porcine DNA.

Analisis Hasil Isolasi DNA dari Bulu Ayam yang Dicuplik dari Pangkal Bulu Muda, Pangkal Bulu Tua dan Ujung Bulu Alfi Sophian
BIOEDUSCIENCE Vol 5 No 2 (2021): BIOEDUSCIENCE
Publisher : Universitas Muhammadiyah Prof. Dr. Hamka

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22236/j.bes/526211

Background: The goal was to provide information on the use of DNA templates in chicken samples so that the molecular research sampling process may employ feathers instead of hurting the test animals. Method: The sample used consisted of 10 Bangkok chickens which were sampled for young feathers and old feathers and the tips of the feathers. Quantitative techniques by comparing the results of DNA isolation which were analyzed using a nano photometer and then confirmed using real-time PCR with the SYBR green method. Result: The analysis of purity and concentration showed that at the base of young chicken feathers, the average value of purity was at 1,790, with an average value of the concentration of 4,210. At the base of the old feather, the average value of purity was 0.638, with an average concentration value that was not detected. Likewise, at the tip of the feather, the average purity value is 0.894 and the concentration value is not detected. Confirmation tests performed on all samples using the real-time PCR melt curve method showed that all samples were detected with a Tm value of 78.5 for young feathers, 78.5 for old feathers, 79.0 for positive controls and 78.7 for positive controls, while negative controls were not detected. Conclusion: DNA isolation can be carried out at the base of the young feathers, the base of the old feathers and the tips of the feathers.

Detection of Salmonella typhimurium ATCC 14028 in Powder Prepared Traditional Medicines Using Real-Time PCR Alfi Sophian; Ratna Purwaningsih; Muindar Muindar; Eka Putri Juniarti Igirisa; Muhammad Luthfi Amirullah
Borneo Journal of Pharmacy Vol. 4 No. 3 (2021): Borneo Journal of Pharmacy
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/bjop.v4i3.1838

The detection of Salmonella typhimurium ATCC 14028 using real-time PCR on powdered traditional medicinal products was carried out in the microbiology and molecular biology testing laboratory of the Food and Drug Administration in Gorontalo. This research aims to provide a reference for alternative testing methods in testing the products of traditional powder preparations on the market. The sample consisted of 10 traditional powder preparations spiked with positive control of S. typhimurium ATCC 14028 phase 2. The method used in the study was real-time PCR analysis using the SYBR® Green method, while DNA isolation using the direct PCR method. Data analysis was performed by analyzing the sample's melting temperature (Tm) curve and comparing it with positive control. The results showed that S. typhimurium ATCC 14028 was detected in samples at an average Tm value of 84.18°C, with ranges of 84.0-84.5°C. For positive control, the Tm value was at 85.2°C, while for the negative control, the Tm value was not detected. Based on these data, it can be concluded that S. typhimurium ATCC 14028 in traditional medicine products powder preparations can be detected using real-time PCR.

Use of Direct PCR Technique Without DNA Extraction in Confirmation Test for Salmonella typhimurium Bacteria on Meatball Samples Alfi Sophian; Ratna Purwaningsih; Muindar Muindar; Eka Putri Juniarti Igirisa; Muhammad Luthfi Amirullah
Borneo Journal of Pharmacy Vol. 4 No. 4 (2021): Borneo Journal of Pharmacy
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33084/bjop.v4i4.2187

The use of direct PCR technique without DNA extraction in the confirmation test for Salmonella typhimurium ATCC 14028 bacteria on meatball samples was carried out in the Food and Drug molecular biology testing laboratory Administration in Gorontalo. The basis of this research is to have an impact on economic value in carrying out the confirmation test for S. typhimurium ATCC 14028, where testing is carried out conventionally, namely DNA extraction, which requires a large amount of money. Hence, it is necessary to innovate to modify the testing phase so that it is more effective and efficient. The purpose of this study was to see whether the direct PCR technique without DNA extraction can be done for the confirmation test of S. typhimurium ATCC 14028 on meatball samples. This study's sample consisted of 20 types of meatball samples spiked with S. typhimurium ATCC 14028 cultures. The method used in this study was qPCR analysis using the SYBR Green method. Data analysis was carried out based on 2 main criteria: (1) Ct analysis and (2) Tm analysis. Real-time PCR analysis results obtained Ct values in the range 14.14 - 15.20 with an average of 14.82 and Tm values 85.20 - 86.30 with an average of 85.79. Based on these data, it can be concluded that using direct PCR can be used for testing confirmation of S. typhimurium ATCC 14028 on meatball samples.

Analisis Hasil Isolasi DNA dari Bulu Ayam yang Dicuplik dari Pangkal Bulu Muda, Pangkal Bulu Tua dan Ujung Bulu Alfi Sophian
BIOEDUSCIENCE Vol 5 No 2 (2021): BIOEDUSCIENCE
Publisher : Universitas Muhammadiyah Prof. Dr. Hamka

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22236/j.bes/526211

Background: The goal was to provide information on the use of DNA templates in chicken samples so that the molecular research sampling process may employ feathers instead of hurting the test animals. Method: The sample used consisted of 10 Bangkok chickens which were sampled for young feathers and old feathers and the tips of the feathers. Quantitative techniques by comparing the results of DNA isolation which were analyzed using a nano photometer and then confirmed using real-time PCR with the SYBR green method. Result: The analysis of purity and concentration showed that at the base of young chicken feathers, the average value of purity was at 1,790, with an average value of the concentration of 4,210. At the base of the old feather, the average value of purity was 0.638, with an average concentration value that was not detected. Likewise, at the tip of the feather, the average purity value is 0.894 and the concentration value is not detected. Confirmation tests performed on all samples using the real-time PCR melt curve method showed that all samples were detected with a Tm value of 78.5 for young feathers, 78.5 for old feathers, 79.0 for positive controls and 78.7 for positive controls, while negative controls were not detected. Conclusion: DNA isolation can be carried out at the base of the young feathers, the base of the old feathers and the tips of the feathers.

Detection for Salmonella typhimurium ATCC 14028 on Sausage, Nugget, Meatballs, Otak-Otak, Tempura and Cilok Products Using the Kit Rapid Test Sophian, Alfi; Muindar, Muindar
Journal of Experimental and Clinical Pharmacy (JECP) Vol 1, No 1 (2021): February, 2021
Publisher : Poltekkes Kemenkes Gorontalo

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52365/jecp.v1i1.198

Testing for Salmonella typhimurium ATCC 14028 using a rapid test kit was carried out in the microbiology and molecular biology testing laboratory of the Food and Drug Administration in Gorontalo. Research using a rapid test kit is a simple study that requires a relatively shorter time than using conventional techniques. The purpose of this study was to see the work of the rapid test kit in detecting Salmonella typhimurium ATCC 14028 spiked on several food processed products. The sample consisted of 12 replications with 6 types of food products including sausages, nuggets, meatballs, otak-otak, tempura and cilok. Positive controls were made from Salmonella typhimurium ATCC 14028 phase 2 cultures, while negative controls used sterilized samples of sausage, nuggets, meatballs, otak-otak, tempura and cilok samples. The concentration of positive control used was taken from turbid work culture and equalized according to Macfarland standard 1. The data analysis was performed qualitatively based on the change in the colour of the kit in the sample which was compared to positive and negative controls. Based on the results of the study, it was found that all samples were detected Salmonella typhimurium ATCC 14028. This study concludes that the rapid test kit can be used to detect Salmonella typhimurium ATCC 14028 in sausage products, nuggets, meatballs, otak-otak, tempura and cilok

Deteksi DNA Spesies pada Produk Makanan Olahan Daging Ayam Menggunakan Gen GH (Growth Hormone) sebagai Penanda Molekuler Sophian, Alfi; Utaminingsih, Sri; Yenita, Yenita; Purwaningsih, Ratna
Food Scientia : Journal of Food Science and Technology Vol 4 No 1 (2024): January - June
Publisher : LPPM Universitas Terbuka

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.33830/fsj.v4i1.6358.2024

The species DNA detection test in processed chicken meat food products using genetic growth hormone (GH) gene markers is a novel approach for authenticity test regarding the presence of a particular species in a product. This research aimed to test the ability of the GH genetic marker to detect the presence of chicken species in processed chicken meat food products. The method used in this research is a molecular biology method using real-time PCR with the SYBR Green kit. The genetic marker primers used were designed independently from the NCBI website. Based on DNA isolation data, the DNA concentration value is 43.60 ng/µL – 45.20 ng/µL with an average of 44.11. The purity value of isolated DNA is 1.855 – 1.925 with an average of 1.906. Chicken species DNA was detected in all samples using real-time PCR analysis, with a Ct value of 24.50 and a Tm value of 78.10. However, the Ct and Tm values were not detected in the negative control (NTC) and specificity (internal) control samples. In the positive control LOD, the Ct value was detected at 27.20 with a Tm value of 79.40. In the positive control, a Ct value of 21.10 and a Tm value of 78.10 were detected. The results indicate that all samples contained the GH gene, and hence, chicken species DNA was detected in all samples. This suggests that the GH genetic marker can be potentially used for species DNA identification testing.

Species DNA Detection Using PGR Gene Genetic Markers in Chicken Nuggets: Species DNA Detection Using PGR Gene Genetic Markers in Chicken Nuggets Sophian, Alfi
Indonesian Food Science and Technology Journal Vol. 5 No. 1 (2021): Volume 5. Nomor 1, December 2021 |IFSTJ|
Publisher : Department of Technology of Agricultural product (THP) Jambi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22437/ifstj.v5i1.14618

Species DNA detection using genetic markers of the PGR gene on chicken nuggets was carried out to see whether these genetic markers could be used to test species DNA detection in chicken nuggets food products. The test method used in this study is a real-time PCR test method using the SYBR green technique where the test results can be either Ct or Tm values â€‹â€‹which indicate amplification or detection. The results of DNA isolation showed that the concentration and purity of the isolated DNA were in the range of 35.10 ng/ÂµL â€“ 36.10ng/ÂµL with an average of 35,488 ng/ÂµL. As for the purity value measured at the A260/A280 wavelength, the results were obtained with a purity range between 2,110 â€“ 2,250 with an average of 2,165. For the results of real-time PCR amplification, the Ct value of the chest sample was at 24.50, the Ct LOD value was at 21.20 and the Ct value of the positive control was 27.10. For the Tm value of the busty sample at 81.10, the Tm LOD value at 81.20 and the positive control Tm value at 82.10. In a conclusion, in this study, genetic markers of the PGR gene can be used to test specific DNA detection of chicken species in chicken nugget products.

Detection of Lysteria monocytogenes in Frozen Meatballs Using Real-Time PCR Sophian, Alfi; Purwaningsih, Ratna
Indonesian Food Science and Technology Journal Vol. 6 No. 1 (2022): Volume 6. Number 1, December 2022 |IFSTJ|
Publisher : Department of Technology of Agricultural product (THP) Jambi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22437/ifstj.v6i1.20391

Detection of pathogenic bacteria Listeria monocytogenes in processed food products of frozen meatballs is one of the critical test parameters in product quality testing. The challenge in testing product quality is how to find a reliable and effective test method to generate test results data. With this research, it is hoped that it can provide information or references for similar research. The method used in this research is the enrichment method with a direct isolation technique and amplification using real-time PCR. Data analysis was carried out based on 2 main criteria which included: (1) Ct analysis (Cycle threshold) and (2) melting temperature (Tm) analysis. From the results of the analysis using real-time PCR, the results of the tested samples were detected at Ct 11.60 with a Tm value of 81.50. For NTC control not detected, this indicates that the master mix used is in good condition and no contamination occurred when testing the sample. The use of this NTC control plays an important role in monitoring the quality of the master mic and test run. For the LOD control and positive control, the results were detected, whereas in the LOD control, the Ct value was detected at 10.08 and the Tm value was at 81.30. for positive control, the value of Ct was detected at 10.85 and the value of Tm was at 82.0. Based on the results of the study, it can be concluded that the test method used can detect Listeria monocytogenes in processed meat products in the form of frozen meatballs.

Limit of Detection Test on Salmonella spp testing on Processed Food Products Egg Pindang According to ISO 16140-3: 2021 Eni Cahyaningsih; Aditya Anugerah Marusaha Sitorus; Alfi Sophian
Keluwih: Jurnal Sains dan Teknologi Vol. 4 No. 2 (2023): Keluwih: Jurnal Sains dan Teknologi (August)
Publisher : Direktorat Penerbitan dan Publikasi Ilmiah, Universitas Surabaya

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24123/saintek.v4i2.5796

Abstract—The development of pathogenic bacteria detection methods in food products has led to the emergence of faster, shorter, and more efficient techniques. However, when choosing a reference method for testing, it is crucial to ensure its reliability. The purpose of this study was to determine the limit of detection (LOD) for Salmonella testing in processed chicken egg food products (Pindang Egg). The research aims to provide valuable information and serve as a reference for similar studies. The method used in this study follows ISO 6579-1:2017, while the detection limit is determined according to ISO 16140-3:2021. The results from observations on pre-enrichment and enrichment media showed that all inoculated samples exhibited a color change to cloudy, indicating bacterial growth in the media. Isolation on selective media and conformational tests confirmed 100% positivity for all samples in contamination variations of 11, 3.67, and 1.22. However, for contamination variation of 0.41, only 75% of the analyzed test data detected the presence of Salmonella, with 1 out of 4 replications not detecting it (approximately 20% failure rate). In conclusion, the lowest LOD value that can be reliably detected is 100% in the contamination variation of 1.22, while for the 0.41 variation, the detection rate only reaches 75% of the analyzed test data. Keywords: bacteria, eggs, pathogen, salmonella Abstrak—Pengembangan metode deteksi bakteri patogen dalam produk pangan telah menghasilkan teknik yang lebih cepat, lebih singkat, dan lebih efisien. Namun, saat memilih metode referensi untuk pengujian, sangat penting untuk memastikan kehandalannya. Tujuan dari penelitian ini adalah untuk menentukan batas deteksi (LOD) untuk pengujian Salmonella dalam produk pangan telur ayam olahan (Pindang Egg). Penelitian ini bertujuan untuk memberikan informasi berharga dan menjadi referensi untuk penelitian serupa. Metode yang digunakan dalam penelitian ini mengikuti ISO 6579-1:2017, sementara batas deteksinya ditentukan sesuai dengan ISO 16140-3:2021. Hasil pengamatan pada media pra-pemupukan dan pemupukan menunjukkan bahwa semua sampel yang diinokulasi menunjukkan perubahan warna menjadi keruh, menandakan pertumbuhan bakteri dalam media. Isolasi pada media selektif dan uji konformasi mengkonfirmasi positivitas 100% untuk semua sampel dalam variasi kontaminasi sebesar 11, 3,67, dan 1,22. Namun, untuk variasi kontaminasi sebesar 0,41, hanya 75% data uji yang dianalisis mendeteksi keberadaan Salmonella, dengan 1 dari 4 replikasi tidak mendeteksinya (sekitar 20% tingkat kegagalan). Sebagai kesimpulan, nilai LOD terendah yang dapat dideteksi dengan handal adalah 100% dalam variasi kontaminasi sebesar 1,22, sementara untuk variasi 0,41, tingkat deteksinya hanya mencapai 75% dari data uji yang dianalisis. Kata kunci: bakteri, telur, patogen, salmonella

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